Chloe Zubieta, Markus Schmid, Vanessa M. Conn, Aditya Nayak, Véronique Hugouvieux, Agnès Jourdain, Simon J. Conn, Gökhan Cildir, Giovanna Capovilla, Vinay Tergaonkar, Stephanie A. Conos, Centre for Cancer Biology, Hanson Institute, Adelaide, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Biochemistry, Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore (NUS), Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, ANR (FLOPINET), CNRS, NHMRC [GNT1089167], Australian Research Council [FT160100318], ATIP-Avenir, LabEx GRAL [ANR-10-LABX-49-01], South Australian Government Department of State Development, CEA Irtelis fellowship, ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors(2016), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Conn, Vanessa M, Hugouvieux, Véronique, Nayak, Aditya, Conos, Stephanie A, Capovilla, Giovanna, Cildir, Gökhan, Jourdain, Agnés, Tergaonkar, Vinay, Schmid, Markus, Zubieta, Chloe, Conn, Simon J, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors, and ANR-10-LABX-49-01,Labex GRAL
Simon J. Conn (simon.conn@unisa.edu.au); International audience; Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as $bona\ fide$ biomarkers of functional, exon-skipped AS variants in $Arabidopsis$, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.